Recent molecular evidence has shown that the largest genus of the family Hipposideridae, Hipposideros, is paraphyletic with respect to H. commersonii sensu lato and H. vittatus, both belonging to a species complex referred to as the commersonii group. The taxonomic issues at the generic level of certain species of Hipposideros remain unresolved in part related to insufficient material in previous molecular studies. Herein, we expand sampling of the commersonii group and include H. commersonii sensu stricto from its type locality, Madagascar. Our phylogenetic analysis revealed that the commersonii group forms a highly supported monophyletic clade with H. cyclops, which is sister taxa to Aselliscus and Coelops. A combination of phylogenetic and comparative morphological analyses, as well as divergence time estimates, were used to provide compelling evidence to support the placement of the clade containing the commersonii group and that with H. cyclops in two resurrected genera, Macronycteris and Doryrhina, respectively. Divergence time estimates indicated that Macronycteris and Doryrhina diverged 19 mya and separated from Coelops and Aselliscus in the Oligocene, about 31 mya. The commersonii group underwent a rapid radiation as recently as 3 mya likely in response to favourable climatic conditions during the Late Pliocene in Africa. Phylogenetic analysis of Cyt-b could not resolve relationships within this morphologically conserved complex. Further sampling is necessary to fully elucidate the evolutionary history of Doryrhina. Given that cryptic species are widespread among bats, including within the genus Hipposideros, this study highlights the shortcomings of current chiropteran taxonomy to describe hidden diversity.